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- PDB-5cpn: Crystal structure of XenA from Pseudomonas putida in complex with... -

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Basic information

Entry
Database: PDB / ID: 5cpn
TitleCrystal structure of XenA from Pseudomonas putida in complex with an NADH mimic (mAc)
ComponentsXenobiotic reductase
KeywordsOXIDOREDUCTASE / XenA / mNADH mimic
Function / homology
Function and homology information


NADPH dehydrogenase activity / FMN binding / NADP binding / metal ion binding
Similarity search - Function
NADPH dehydrogenase YqjM-like / NADH:flavin oxidoreductase/NADH oxidase, N-terminal / NADH:flavin oxidoreductase / NADH oxidase family / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
1-[(3S)-1-benzylpiperidin-3-yl]ethanone / Chem-FNR / Xenobiotic reductase
Similarity search - Component
Biological speciesPseudomonas putida (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsKnaus, T. / Paul, C.E. / Levy, C.W. / Mutti, F.G. / Hollmann, F. / Scrutton, N.S.
CitationJournal: J.Am.Chem.Soc. / Year: 2016
Title: Better than Nature: Nicotinamide Biomimetics That Outperform Natural Coenzymes.
Authors: Knaus, T. / Paul, C.E. / Levy, C.W. / de Vries, S. / Mutti, F.G. / Hollmann, F. / Scrutton, N.S.
History
DepositionJul 21, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jan 20, 2016Provider: repository / Type: Initial release
Revision 1.1Feb 3, 2016Group: Database references
Revision 1.2Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Xenobiotic reductase
B: Xenobiotic reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,2806
Polymers81,9282
Non-polymers1,3514
Water9,584532
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4600 Å2
ΔGint-32 kcal/mol
Surface area24050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.370, 158.050, 57.370
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Xenobiotic reductase / Xenobiotic reductase A


Mass: 40964.086 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas putida (bacteria) / Gene: xenA / Plasmid: pET21A / Production host: Escherichia coli (E. coli) / References: UniProt: Q9R9V9
#2: Chemical ChemComp-531 / 1-[(3S)-1-benzylpiperidin-3-yl]ethanone


Mass: 217.307 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H19NO
#3: Chemical ChemComp-FNR / 1-DEOXY-1-(7,8-DIMETHYL-2,4-DIOXO-3,4-DIHYDRO-2H-BENZO[G]PTERIDIN-1-ID-10(5H)-YL)-5-O-PHOSPHONATO-D-RIBITOL / TWO ELECTRON REDUCED FLAVIN MONONUCLEOTIDE


Mass: 458.360 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H23N4O9P
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 532 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.33 Å3/Da / Density % sol: 47.31 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.2 M calcium acetate, 0.1 M sodium cacodylate buffer pH 6.5, 40% v/v PEG 300 (JCSG+ HT96 A10 Molecular Dimensions)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 17, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.8→57.37 Å / Num. obs: 71667 / % possible obs: 100 % / Redundancy: 7.8 % / Rmerge(I) obs: 0.1454 / Net I/σ(I): 8.9
Reflection shellResolution: 1.8→1.864 Å / Redundancy: 8.2 % / Rmerge(I) obs: 1.639 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIXdev_1977refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2H90

2h90


Resolution: 1.8→57.37 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 27.31 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2187 3602 5.03 %Random
Rwork0.182 ---
obs0.1838 71640 99.59 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.8→57.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5552 0 94 532 6178
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0125848
X-RAY DIFFRACTIONf_angle_d1.3637985
X-RAY DIFFRACTIONf_dihedral_angle_d14.7742053
X-RAY DIFFRACTIONf_chiral_restr0.072838
X-RAY DIFFRACTIONf_plane_restr0.0081045
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8001-1.82380.35211440.34442556X-RAY DIFFRACTION99
1.8238-1.84870.34631190.33862618X-RAY DIFFRACTION100
1.8487-1.87520.37381380.33052557X-RAY DIFFRACTION99
1.8752-1.90310.37041190.30282594X-RAY DIFFRACTION99
1.9031-1.93290.31841330.28942576X-RAY DIFFRACTION100
1.9329-1.96460.31491420.27382584X-RAY DIFFRACTION99
1.9646-1.99850.30371410.27252592X-RAY DIFFRACTION99
1.9985-2.03480.26381230.25782601X-RAY DIFFRACTION100
2.0348-2.07390.27511360.24332575X-RAY DIFFRACTION99
2.0739-2.11630.25971420.2312579X-RAY DIFFRACTION99
2.1163-2.16230.29391290.20882597X-RAY DIFFRACTION100
2.1623-2.21260.22311340.20352611X-RAY DIFFRACTION99
2.2126-2.26790.24721250.19272609X-RAY DIFFRACTION100
2.2679-2.32920.26641520.19672568X-RAY DIFFRACTION99
2.3292-2.39780.27121390.18622594X-RAY DIFFRACTION100
2.3978-2.47520.23951550.18832609X-RAY DIFFRACTION100
2.4752-2.56360.23881410.17832596X-RAY DIFFRACTION100
2.5636-2.66630.21481440.17792620X-RAY DIFFRACTION100
2.6663-2.78760.19991500.17762606X-RAY DIFFRACTION100
2.7876-2.93460.25881510.17892622X-RAY DIFFRACTION100
2.9346-3.11850.21121210.17822641X-RAY DIFFRACTION100
3.1185-3.35920.20581380.16842683X-RAY DIFFRACTION100
3.3592-3.69720.17441380.15132630X-RAY DIFFRACTION100
3.6972-4.23210.18251230.13872704X-RAY DIFFRACTION100
4.2321-5.33140.14591630.12642688X-RAY DIFFRACTION100
5.3314-57.70580.17751620.16532828X-RAY DIFFRACTION100

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